Try scraping the cappings off the honey (be sure to damage the rest of the comb in the super slightly as well). This will force them to move it and store it elsewhere. Remove the super later if it bothers you.
Personally, I leave an extra super on. Its there if they need it and if they don't, ill just harvest it in spring.

Get a large (turkey size) crock pot from a thrift store. Add 2 inches of water, melt, skim the surface with a hand strainer. (You get better results if you simply melt it, not boil it) Let cool and pour out trashy water. Remelt, then pour it through cheese cloth. Cappings come out a great clean yellow, perfect for candles, we make these all the time. When selling the candles, we package them nicely and sell them @ about $2 per ounce. People love them!

Place rubber large bands around the frames and slide the larger chunks of comb back in. They will reconnect it. Melt down whatever cant be put back.
(After you leave it outside for the bees to clean up)

Dont extract those frames you pull, until AFTER they draw the new comb. Some of my hives have stopped drawing comb and refuse to take the 1:1 syrup. So you might need those frames you are about to remove.

Talk to the people in your beekeepers association. I know in my area (SE VA), we need to ensure that the bees have at least 70 lbs of honey to make it through the winter. It is usually considered bad practice to pull honey within a hives first year.

I don't know about your areas winters, but here we suggest wintering with a minimum of two full deeps. Personally, i add a super for safe measure. It really would be best to contact/join your local beekeepers association and ask them what is the best practice in your region.

You need to check the bottom boxes. The foragers (probably) filled in the lower comb, forcing the queen upwards. You need to know how much the have stored, so you know whether to continue feeding or not.